Phylogenetic Study of Local Patterns Influenza A(H3N2) Virus Transmission in a Semi-Isolated Population in a Remote Island in Japan Between 2011 and 2013

IF 4.3 4区医学 Q1 INFECTIOUS DISEASES Influenza and Other Respiratory Viruses Pub Date : 2025-03-10 DOI:10.1111/irv.70089

Su Myat Han, Teiichiro Shiino, Shingo Masuda, Yuki Furuse, Takahiro Yasaka, Satoshi Kanda, Kazuhiri Komori, Nobuo Saito, Yoshiano Kubo, Chris Smith, Akira Endo, Alexis Robert, Marc Baguelin, Koya Ariyoshi

{"title":"Phylogenetic Study of Local Patterns Influenza A(H3N2) Virus Transmission in a Semi-Isolated Population in a Remote Island in Japan Between 2011 and 2013","authors":"Su Myat Han, Teiichiro Shiino, Shingo Masuda, Yuki Furuse, Takahiro Yasaka, Satoshi Kanda, Kazuhiri Komori, Nobuo Saito, Yoshiano Kubo, Chris Smith, Akira Endo, Alexis Robert, Marc Baguelin, Koya Ariyoshi","doi":"10.1111/irv.70089","DOIUrl":null,"url":null,"abstract":"<div>\n \n \n <section>\n \n <h3> Background</h3>\n \n <p>Influenza A outbreak risk is impacted by the potential for importation and local transmission. Reconstructing transmission history with phylogenetic analysis of genetic sequences can help assess outbreak risk but relies on regular collection of genetic sequences. Few influenza genetic sequences are collected in Japan, which makes phylogenetic analysis challenging, especially in rural, remote settings. We generated influenza A genetic sequences from nasopharyngeal swabs (NPS) samples collected using rapid influenza diagnostic tests and used them to analyze the transmission dynamics of influenza in a remote island in Japan.</p>\n </section>\n \n <section>\n \n <h3> Methods</h3>\n \n <p>We generated 229 whole genome sequences of influenza A/H3N2 collected during 2011/12 and 2012/13 influenza seasons in Kamigoto Island, Japan, of which 178 sequences passed the quality check. We built time-resolved phylogenetic trees from hemagglutinin sequences to classify the circulating clades by comparing the Kamigoto sequences to global sequences. Spatiotemporal transmission patterns were then analyzed for the largest local clusters.</p>\n </section>\n \n <section>\n \n <h3> Results</h3>\n \n <p>Using a time-resolved phylogenetic tree, we showed that the sequences clustered in six independent transmission groups (1 in 2011/12, 5 in 2012/13). Sequences were closely related to strains from mainland Japan. All 2011/12 strains were identified as clade 3C.2 (<i>n</i> = 29), while 2012/13 strains fell into two clades: clade 3C.2 (<i>n</i> = 129) and 3C.3a (<i>n</i> = 20). Clusters reported in 2012/13 circulated simultaneously in the same regions. The spatiotemporal analysis of the largest cluster revealed that while the first sequences were reported in the busiest district of Kamigoto, the later sequences were scattered across the island.</p>\n </section>\n \n <section>\n \n <h3> Conclusion</h3>\n \n <p>Kamigoto Island was exposed to repeated importations of Influenza A(H3N2), mostly from mainland Japan, sometimes leading to local transmission and ultimately outbreaks. As independent groups of sequences overlapped in time and space, cases may be wrongly allocated to the same transmission group in the absence of genomic surveillance, thereby underestimating the risk of importations. Our analysis highlights how NPS could be used to better understand influenza transmission patterns in little-studied settings and improve influenza surveillance in Japan.</p>\n </section>\n </div>","PeriodicalId":13544,"journal":{"name":"Influenza and Other Respiratory Viruses","volume":"19 3","pages":""},"PeriodicalIF":4.3000,"publicationDate":"2025-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/irv.70089","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Influenza and Other Respiratory Viruses","FirstCategoryId":"3","ListUrlMain":"https://onlinelibrary.wiley.com/doi/10.1111/irv.70089","RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"INFECTIOUS DISEASES","Score":null,"Total":0}

引用次数: 0

Abstract

Background

Influenza A outbreak risk is impacted by the potential for importation and local transmission. Reconstructing transmission history with phylogenetic analysis of genetic sequences can help assess outbreak risk but relies on regular collection of genetic sequences. Few influenza genetic sequences are collected in Japan, which makes phylogenetic analysis challenging, especially in rural, remote settings. We generated influenza A genetic sequences from nasopharyngeal swabs (NPS) samples collected using rapid influenza diagnostic tests and used them to analyze the transmission dynamics of influenza in a remote island in Japan.

Methods

We generated 229 whole genome sequences of influenza A/H3N2 collected during 2011/12 and 2012/13 influenza seasons in Kamigoto Island, Japan, of which 178 sequences passed the quality check. We built time-resolved phylogenetic trees from hemagglutinin sequences to classify the circulating clades by comparing the Kamigoto sequences to global sequences. Spatiotemporal transmission patterns were then analyzed for the largest local clusters.

Results

Using a time-resolved phylogenetic tree, we showed that the sequences clustered in six independent transmission groups (1 in 2011/12, 5 in 2012/13). Sequences were closely related to strains from mainland Japan. All 2011/12 strains were identified as clade 3C.2 (n = 29), while 2012/13 strains fell into two clades: clade 3C.2 (n = 129) and 3C.3a (n = 20). Clusters reported in 2012/13 circulated simultaneously in the same regions. The spatiotemporal analysis of the largest cluster revealed that while the first sequences were reported in the busiest district of Kamigoto, the later sequences were scattered across the island.

Conclusion

Kamigoto Island was exposed to repeated importations of Influenza A(H3N2), mostly from mainland Japan, sometimes leading to local transmission and ultimately outbreaks. As independent groups of sequences overlapped in time and space, cases may be wrongly allocated to the same transmission group in the absence of genomic surveillance, thereby underestimating the risk of importations. Our analysis highlights how NPS could be used to better understand influenza transmission patterns in little-studied settings and improve influenza surveillance in Japan.

Abstract Image

查看原文

微信好友朋友圈 QQ好友复制链接

本刊更多论文

求助全文

约1分钟内获得全文去求助

来源期刊

Influenza and Other Respiratory Viruses 医学-病毒学

CiteScore

7.20

自引率

4.50%

发文量

120

审稿时长

6-12 weeks

期刊介绍： Influenza and Other Respiratory Viruses is the official journal of the International Society of Influenza and Other Respiratory Virus Diseases - an independent scientific professional society - dedicated to promoting the prevention, detection, treatment, and control of influenza and other respiratory virus diseases. Influenza and Other Respiratory Viruses is an Open Access journal. Copyright on any research article published by Influenza and Other Respiratory Viruses is retained by the author(s). Authors grant Wiley a license to publish the article and identify itself as the original publisher. Authors also grant any third party the right to use the article freely as long as its integrity is maintained and its original authors, citation details and publisher are identified.